Added --pp-filter-off argument to switch off filter DNM_PP > 0.9
Updated the new PP_DNM filter argument to pass in the threshold rather than a boolean.  Can be set to zero to allow all to pass
added option to specify a variant to debug, rather than hardcoding this
added unit tests for the new PP_dnm filter option
unit tested the debugging options
clean up code for merging master
minor adjustment to previous commit